Pubtator

liveBooks

PubTator 3 MCP — biomedical entity search, literature search with entity highlighting, and entity-entity relations with supporting passages, from the PubTator 3 API run by NCBI / NLM (National Library of Medicine).

5tools
0msauth
free tier50 calls/day

Tools

pubtator_find_entity

Resolve a gene, disease, chemical/drug, variant, species or cell-line name to its normalized PubTator 3 entity id (e.g. "BRCA1" -> @GENE_BRCA1, NCBI Gene 672; "breast cancer" -> @DISEASE_Breast_Neopla

No parameters required.

▶Try it
pubtator_relations

List the relations PubTator 3 has extracted for a gene, disease, chemical or variant — which drugs treat a disease, which genes a disease is associated with, which chemicals inhibit a gene — ranked by

No parameters required.

▶Try it
pubtator_relation_evidence

The supporting passages behind one specific PubTator 3 relation — every paper whose text the model read the relation from, with the matched sentence, both entities' mentions, PMID, journal and date. G

No parameters required.

▶Try it
pubtator_annotations

Entity annotations for specific PubMed articles: every gene, disease, chemical, variant, species and cell-line mention in the title and abstract (or PMC full text), each normalized to NCBI Gene / MeSH

No parameters required.

▶Try it

Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/pubtator/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/pubtator/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"pubtator_find_entity","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("pubtator_find_entity", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("pubtator 3 mcp — biomedical entity search, literature search with entity highlighting, and entity-entity relations with supporting passages, from the pubtator 3 api run by ncbi / nlm (national library of medicine)");